Dear community.
I'm just studying for a master’s degree in the department of biochemical science & technology, at National Taiwan University.
When I try to refine the structure at Coot or search the paper about the protein structure or membrane protein.
I'm curious about what is the meaning of Fo and Fc, and the difference between the Fo-Fc map and the 2Fo-Fc map their meaning.
Why they are important when we try to fit the residues or molecules in electron density maps?
Also, I what to know does it has any program or application that can create the density map in this journal article.
The supplementary figure 6 in Astashkin, R., Kovalev, K., Bukhdruker, S. et al.Structural insights into light-driven anion pumping in cyanobacteria. Nat Commun 13, 6460 (2022). https://doi.org/10.1038/s41467-022-34019-9
It's my first time asking the question on this website and I’m not an English native speaker, sorry if I offended you.
Cordially,
Guan-Yi.
Fo is the observed electron density , Fc the electron density calculated from the structure model built into the observed density. The Fo-Fc difference map compares the two by calculating the difference between the observed and calculated electron density. If your structure model would perfectly fit the observed experimental density, the Fo-Fc difference map would be close to zero everywhere. Peaks in (Fo-Fc) highlight places where the structure model cannot explain the observed electron density, and where you have to improve your model. See https://proteopedia.org/wiki/index.php/Electron_density_maps and papers cited there. In the supplementary figure 6 the Fo derived from two different experiments are compared to evaluate conformational differences between the ground state and a light-activated state of the protein.
The electron-density map is the Fourier transform of the structure factors (with their phases).
2Fo-Fc is the best way to calculate an estimate of the true electron density from diffraction data and atomic model. (It is called 2Fo-Fc because the calculation involves combining the observed diffraction data, Fo, with the diffraction data calculated from the atomic model, Fc, in a way that gives the least-biased result).
https://proteopedia.org/wiki/index.php/Electron_density_maps
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